Those of you who have trouble with the V2.5 cores, please report if you have a PAL or an NTSC crystal in your host machine. PAL machines use 28,37516MHz and NTSC machines use 28,65656MHz.
The difference is that on some FPGAs, the PAL crystal generates a too-low VCO frequency for the internal PLL. It's off by less than 1%, but it might cause trouble. Only two output pixel clocks are "on the edge": 59,8621MHz and 149,6552MHz.
If you suspect that this is the cause for your machine, then delete these two files:
coreMK2C25_B21.rbf (the 149,6552 MHz core)
coreMK2C25_E21.rbf (the 59,8621 MHz core)
In any case, please make sure that the V2.4 cores are removed from the directory, and that you don't mix config files from the old tool with the new release.